"It's very classic, this pattern," Kelly says. "We've seen hundreds of cases over the last couple of years at our program."

Kelly's program specializes in the microbes that live in our digestive systems — trillions of bacteria, viruses, fungi and other mostly helpful microbes whose genes scientists collectively call the human microbiome.

The problem, she told Iverson, started when antibiotics prescribed for another health problem disrupted the community of benign organisms in her intestines, leaving her vulnerable to a really bad bug — a bacterium called Clostridium difficile.

"You can almost look at C. diff as ... the prototypical example," Kelly says, of how a disruption in the human microbiome can result in disease.

Kelly is among a growing number of doctors who are starting to use what scientists are learning about our microbiomes to help prevent, diagnose, and treat many illnesses. For Iverson, she proposed something that may sound pretty radical — what doctors call a fecal transplant.

"It's really almost like an organ transplant," Kelly says. "You're taking this whole community of microorganisms from one person, [and] transplanting them into another person. Then these things ... take root, colonize and kind of restore that balance."

Iverson says she initially found the idea repulsive. But she felt so desperate that she agreed to try it.

"I was scared to death, honey," Iverson says. "I'm an old lady. I've got one foot in the grave and the other on the banana peel."

What happened to Iverson is the most dramatic example of how doctors are manipulating the microbiome in lots of ways to help lots of different kinds of patients.

For one thing, Kelly says doctors are testing the use of the transplants in other illnesses, such as colitis, Crohn's disease and diabetes. And there's even talk of trying the treatment for obesity.

"We're at a really interesting point in medicine where we've come to appreciate the microbiome and that [these organisms] have really integral roles in ... energy metabolism, and immune function, and all of these other things," Kelly says.

At the same time, researchers are looking for more subtle ways to fix our microbiomes. For starters, they're trying to remove the "yuk" factor from microbiome transplants by figuring out exactly which microorganisms patients really need and giving them just those.

And there's tons of research involving so-called probiotics — live cultures of supposedly beneficial microbes, typically included in yogurt or other foods or supplements. Probiotics are meant to be swallowed, in hopes that they'll outcompete pathogenic bacteria and restore a healthy balance.

"The evidence is really mounting to the point where I think it's undeniable that the ingestion of live bacteria — safe bacteria in high numbers — has an overall beneficial effect on human health," says Colin Hill of the University College Cork in Ireland.

Scientists are testing a long list of probiotics for a variety of health problems, including vaginal infections, colic in babies and weakened immune systems in the elderly. They're also studying so-called prebiotics — nondigestible carbohydrates meant as food for the good microbes.

Now, anyone who walks into a grocery store these days knows that hundreds of prebiotic and probiotic products are already on the market. You can't watch TV or go on the Internet without hearing the kinds of claims the manufacturers of these products make.

The companies point to studies supporting their claims. But many experts say there are still huge questions about how safe such products are, how pure they are, and whether they really do what their makers say they do.

"All of those things together open up the opportunity for ... the equivalent of snake oil salesmen related to probiotics or microbial treatments, or fecal transplants or whatever," says Jonathan Eisen of the University of California, Davis.

And Eisen is not alone in his criticism. The Food and Drug Administration has big concerns. Those concerns include whether microbiome transplants might spread infections, or are being promoted for unproven uses, or whether they might actually increase the risk for some health problems.

"The gut microbiome can affect obesity, diabetes [and] a number of other disorders," says Jay Slater, director of the FDA's Division of Bacterial, Parasitic and Allergenic Products. "These are the kinds of concerns that would indicate that good long-term studies really should be done."

So the FDA requires that doctors who want to do microbiome transplants for anything other than C. diff treatment get FDA approval first. And physicians must warn patients that, even for C. diff, the treatment is still experimental. Scientists studying probiotics have to put them through the same careful testing that regular drugs go through.

All this is really frustrating for many scientists. They argue that these regulatory roadblocks are holding up research and making it too hard for patients to get microbiome transplants.

"People are dying of C. diff," says Kelly. "And people are living in this really terrible state. I see people who've lost their jobs, people who've become depressed because of just the feeling of utter hopelessness. And I think it's really unethical to withhold the treatment from patients who need it."

As for Iverson, she agrees that anyone who needs such a transplant should be able to get one.

"I think it's terrific," she says. "I think it's the best thing that ever happened. This is like a step to heaven having this done."

Copyright 2013 NPR. To see more, visit http://www.npr.org/.

Transcript

AUDIE CORNISH, HOST:

From NPR News, this is ALL THINGS CONSIDERED. I'm Audie Cornish.

ROBERT SIEGEL, HOST:

And I'm Robert Siegel. We're going to spend the next few minutes now talking about something very small, but very big when it comes to human health - microorganisms. Those include bacteria, viruses, fungi. Today on MORNING EDITION, NPR's Rob Stein took us on a tour of this microscopic world, not only in your gut but also in your ears, mouth, just about everywhere on your body.

Well, here's Rob again, with a look at how doctors are starting to manipulate microbes to help people stay healthy, and to treat them when they get sick.

ROB STEIN, BYLINE: Billie Iverson may be getting up there. But for an 86-year-old, she's still plenty active.

BILLIE IVERSON: Oh, I take trips, and I go do my own shopping. And I take myself to the doctor. I do everything. I don't let anything stop me.

STEIN: She recently traveled from her home in Rhode Island to visit her son in North Carolina.

IVERSON: And he took me up to the mountains and took me up for a horse and buggy ride around town, with roses and a bottle of bubbly.

STEIN: But one day, something hit her like nothing else - the worst case of the runs ever.

IVERSON: All this stuff just comes out of me just like Niagara Falls. You could not stop it.

STEIN: Nothing helped. It went on for days and weeks, and it just kept coming back again and again. Iverson got so weak, she eventually ended up in a nursing home.

IVERSON: I didn't know. I just thought maybe I wasn't going to make it. I thought I was going to die.

STEIN: Finally, Iverson's daughter took her to see Colleen Kelly, a doctor at Brown University. Dr. Kelly knew right away what was going on

DR. COLLEEN KELLY: It's very classic, this pattern. You know, we've seen hundreds of cases over the past couple of years, at our program.

STEIN: Kelly's program specializes in the microbes that live in our digestive systems; trillions of bacteria and other microbes, helpful microbes scientists call the human microbiome. Kelly knew Iverson's microbiome had gotten messed up by some antibiotics, leaving her vulnerable to a really bad bug; a bug called Clostridium difficile, or C-diff.

KELLY: You can almost look at C-diff as like the prototypical example of how - when you have a disruption in the human microbiome that can result in disease.

STEIN: Kelly is among a growing number of doctors who are starting to use what scientists are learning about our microbiomes to help prevent, diagnose and treat many diseases. So Kelly proposed something that may sound pretty radical, something Iverson still has a hard time even talking about.

IVERSON: This - how are you going to put it? This poop transfer. (Laughing) That's what - that's the only way I know how to put it.

STEIN: Doctors call it a fecal transplant.

IVERSON: Take my poop out, and put somebody else's poop in there. That is the most disgusting thing. I said oh, no way; I said, no way am I doing that.

STEIN: It may sound pretty gross, but Dr. Kelly says it seems to work really well. And it's being done more and more, these days, to treat C-diff.

KELLY: It's really almost like an organ transplant. You're taking this whole community of microorganisms from one person, you're transplanting them into another person. And then these things, you know, take root, colonize, and kind of restore that balance.

STEIN: Iverson was so desperate, she decided to try it.

IVERSON: I was scared to death, honey. I'm an old lady. I've got one foot in the grave, and the other one on the banana peel.

STEIN: The procedure turned out to be really easy. And it worked - pretty much overnight.

STEIN: What happened to Iverson is the most dramatic example of how doctors are manipulating the microbiome in lots of ways, to help lots of different kinds of patients. For one thing, Kelly says doctors are testing the transplants in other illnesses - like colitis, Crohn's and diabetes. And there's even talk of trying them for more conditions, including obesity.

KELLY: We're at a really interesting point in medicine, where we've come to appreciate the microbiome; and that they have really integral roles in like, energy metabolism and immune function, and all of these other things.

STEIN: At the same time, researchers are looking for more subtle ways to fix our microbiomes. For starters, they're trying to take the yuck-factor out of microbiome transplants, by figuring out exactly which microbes patients really need and giving them just those. And there's tons of research involving something we've heard a lot about.

COLIN HALL: Probiotics.

STEIN: Colin Hill studies probiotics at University College Cork, in Ireland.

HALL: The evidence is really mounting to the point where I think it's undeniable that the ingestion of live bacteria, safe bacteria, in high numbers has an overall beneficial effect on human health.

STEIN: Scientists are testing a long list of probiotics for many things: vaginal infections, colicky babies, boosting elderly people's immune systems. They're also studying prebiotics - food for the good microbes.

(SOUNDBITE OF MUSIC IN AD)

STEIN: Now, anyone who walks into a grocery store these days knows hundreds of prebiotics and probiotics are on the market already.

(SOUNDBITE OF AD)

UNIDENTIFIED ANNOUNCER: Our probiotics have been clinically proven to colonize the intestines. This is a powerful type of probiotic...

STEIN: You can't watch TV, or go on the Internet, without hearing the kinds of claims they're making.

(SOUNDBITE OF AD)

UNIDENTIFIED ANNOUNCER: When your gut is healthy, you produce more serotonin, your body's natural chemical that contributes to happiness and well-being.

STEIN: The companies that make these products point to studies supporting their claims. But Jonathan Eisen, of the University of California- Davis, says there are still huge questions about all this - about how safe these products are, how pure they are, and whether they really do what they say they do.

JONATHAN EISEN: All of those things together open up the opportunity for lots of - you know, the equivalent of snake oil salesmen related to probiotics or microbial treatments or fecal transplants, or whatever.

STEIN: And he's not alone. The Food and Drug Administration has big concerns about microbiome transplants spreading infections, being promoted for unproven uses and, according to the FDA's Jay Slater, possibly causing health problems.

JAY SLATER: The gut microbiome can affect obesity, diabetes, a number of other disorders. These are the kinds of concerns that would indicate that good, long-term studies really should be done.

STEIN: So doctors who want to do the procedures for anything other than C-diff have to get the FDA's approval first. And they must warn patients getting them for C-diff that they're still experimental. Scientists studying probiotics have to put them through the same, careful testing that regular drugs go through. All this is really frustrating for many scientists. They argue it's holding up research, and making it too hard for patients to get microbiome transplants. Here's Colleen Kelly again, Billie Iverson's doctor.

KELLY: These people are dying of C-diff, and people are living in this really terrible state. I see people who've lost their jobs, people who've become depressed because of just the feeling of utter hopelessness. And I think that it's really unethical to withhold that treatment from patients who need it.

STEIN: As for Iverson, she agrees that anyone who needs a transplant should be able to get one.

IVERSON: I think it's terrific. I think it's the best thing ever happened. This is like a step to heaven - having this done.

STEIN: There's no doubt that manipulating our microbiomes could help more people like Billie Iverson, and possibly help all of us live longer, healthier lives. The question is whether it's being oversold right now, and how best to harness our microbiomes without doing more harm than good.